diff --git a/pom.xml b/pom.xml index d71d3efe..cafe7403 100644 --- a/pom.xml +++ b/pom.xml @@ -128,7 +128,7 @@ data-model-lib life.qbic - 2.21.0 + 2.24.0 org.mockito diff --git a/src/main/groovy/life/qbic/utils/NanoporeParser.groovy b/src/main/groovy/life/qbic/utils/NanoporeParser.groovy index 7a06610f..3a2b03fc 100644 --- a/src/main/groovy/life/qbic/utils/NanoporeParser.groovy +++ b/src/main/groovy/life/qbic/utils/NanoporeParser.groovy @@ -5,8 +5,10 @@ import groovy.json.JsonSlurper import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutput import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutputV2 import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutputV3 +import life.qbic.datamodel.instruments.OxfordNanoporeInstrumentOutputV4 import org.everit.json.schema.Schema import org.everit.json.schema.ValidationException +import org.everit.json.schema.Validator import org.everit.json.schema.loader.SchemaLoader import org.json.JSONObject import org.json.JSONTokener @@ -184,14 +186,21 @@ class NanoporeParser { try { validateUsingSchema(OxfordNanoporeInstrumentOutputV2.getSchemaAsStream(), jsonObject) } catch (ValidationException validationExceptionV2) { - validateUsingSchema(OxfordNanoporeInstrumentOutputV3.getSchemaAsStream(), jsonObject) + try{ + validateUsingSchema(OxfordNanoporeInstrumentOutputV3.getSchemaAsStream(), jsonObject) + } + catch(ValidationException validationExceptionV3){ + validateUsingSchema(OxfordNanoporeInstrumentOutputV4.getSchemaAsStream(), jsonObject) + } } } } private static void validateUsingSchema(InputStream schemaAsStream, JSONObject jsonObject) throws ValidationException { + //Since we validate multiple schemas we want to fail as early as possible + Validator validator = Validator.builder().failEarly().build() Schema jsonSchema = loadSchemaFromStream(schemaAsStream) - jsonSchema.validate(jsonObject) + validator.performValidation(jsonSchema, jsonObject) } private static Schema loadSchemaFromStream(InputStream stream) { diff --git a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy index 4c9f3327..9d314f0d 100644 --- a/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy +++ b/src/test/groovy/life/qbic/utils/NanoporeParserSpec.groovy @@ -64,6 +64,32 @@ class NanoporeParserSpec extends Specification { assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL" } + def "parsing the a valid file structure with a second basecalling folder returns an OxfordNanoporeExperiment Object"() { + given: + def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v4") + when: + def experiment = NanoporeParser.parseFileStructure(pathToDirectory) + then: + assert experiment instanceof OxfordNanoporeExperiment + // Check that the metadata from the report file has been retrieved + assert experiment.getMeasurements().get(0).getMachineHost() == "PCT0094" + // Check that the metadata from the summary file has been retrieved + assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL" + } + + def "parsing the a valid file structure v4 without basecalling folder returns an OxfordNanoporeExperiment Object"() { + given: + def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4") + when: + def experiment = NanoporeParser.parseFileStructure(pathToDirectory) + then: + assert experiment instanceof OxfordNanoporeExperiment + // Check that the metadata from the report file has been retrieved + assert experiment.getMeasurements().get(0).getMachineHost() == "PCT0094" + // Check that the metadata from the summary file has been retrieved + assert experiment.getMeasurements().get(0).getLibraryPreparationKit() == "SQK-LSK109-XL" + } + def "parsing the alternative valid file structure with metadata missing returns an OxfordNanoporeExperiment Object"() { given: def pathToDirectory = Paths.get(exampleDirectoriesRoot, "validates/QABCD001AB_E12A345a01_PAE12345_nanopore_new_minimal") diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/drift_correction_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/drift_correction_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/duty_time_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/duty_time_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile2.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile3.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile4.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_fail/myfile5.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile2.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile3.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile4.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5 b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5 new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fast5_pass/myfile5.fast5 @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile2.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile3.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile4.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz new file mode 100644 index 00000000..a46c98ae --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_fail/myfile5.fastq.gz @@ -0,0 +1 @@ +This is some text diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile1.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile1.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile2.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile3.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile4.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/fastq_pass/myfile5.fastq.gz new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt new file mode 100644 index 00000000..900f4d7e --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/final_summary_.txt @@ -0,0 +1,17 @@ +instrument=PCT0094 +position=1-A3-D3 +flow_cell_id=PAE24142 +sample_id=QNANO027AE_E19D023a01_200211 +protocol_group_id=20200211_QNANO +protocol=sequencing/sequencing_PRO002_DNA:FLO-PRO002:SQK-LSK109-XL +protocol_run_id=5a7cfc2a-81b0-412d-baa0-51b939cd8e76 +acquisition_run_id=c6028297dff19d01e7c5fba6487de807d1e99c05 +started=2020-02-11T15:52:10.465982+01:00 +acquisition_stopped=2020-02-14T08:39:54.688916+01:00 +processing_stopped=2020-02-14T08:39:58.804639+01:00 +basecalling_enabled=1 +sequencing_summary_file=sequencing_summary_PAE24142_c6028297.txt +fast5_files_in_final_dest=2189 +fast5_files_in_fallback=0 +fastq_files_in_final_dest=2189 +fastq_files_in_fallback=0 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/mux_scan_data_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/mux_scan_data_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md new file mode 100644 index 00000000..586d5325 --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_no_basecalling_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md @@ -0,0 +1,52 @@ +Tracking ID +=========== + +{ + "asic_id": "0004A30B0022C63E", + "asic_id_eeprom": "0004A30B0022C63E", + "asic_temp": "32.631687", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "1.0.7", + "device_id": "1-E9-H9", + "device_type": "promethion", + "distribution_status": "stable", + "distribution_version": "19.12.5", + "exp_script_name": "N/A", + "exp_script_purpose": "sequencing_run", + "exp_start_time": 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+protocol=sequencing/sequencing_PRO002_DNA:FLO-PRO002:SQK-LSK109-XL +protocol_run_id=5a7cfc2a-81b0-412d-baa0-51b939cd8e76 +acquisition_run_id=c6028297dff19d01e7c5fba6487de807d1e99c05 +started=2020-02-11T15:52:10.465982+01:00 +acquisition_stopped=2020-02-14T08:39:54.688916+01:00 +processing_stopped=2020-02-14T08:39:58.804639+01:00 +basecalling_enabled=1 +sequencing_summary_file=sequencing_summary_PAE24142_c6028297.txt +fast5_files_in_final_dest=2189 +fast5_files_in_fallback=0 +fastq_files_in_final_dest=2189 +fastq_files_in_fallback=0 diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/mux_scan_data_.csv b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/mux_scan_data_.csv new file mode 100644 index 00000000..e69de29b diff --git a/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md new file mode 100644 index 00000000..586d5325 --- /dev/null +++ b/src/test/resources/dummyFileSystem/nanopore-instrument-output/validates/QABCD001AB_E12A345a01_PAE12345_nanopore_v4/20200122_1217_1-A1-B1-PAE12345_1234567a/report_.md @@ -0,0 +1,52 @@ +Tracking ID +=========== + +{ + "asic_id": "0004A30B0022C63E", + "asic_id_eeprom": "0004A30B0022C63E", + "asic_temp": "32.631687", + "asic_version": "Unknown", + "auto_update": "0", + "auto_update_source": "https://mirror.oxfordnanoportal.com/software/MinKNOW/", + "bream_is_standard": "0", + "configuration_version": "1.0.7", + "device_id": "1-E9-H9", + "device_type": "promethion", + "distribution_status": 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